That makes no sense. Most subways are built with cut and cover. The Second Avenue was only made possible with the very latest in tunneling technology. And that meant a path being dug carefully around multiple existing subways, lots of other infrastructure, and the relatively delicate foundations of old buildings.
Furthermore, as I pointed out, the extreme impracticality of the Second Avenue subway was documented starting from the first proposal around a hundred years ago which was rejected as being too expensive to make sense. And that was the first of many such studies. Yes, we need to figure out infrastructure and have some problems, but a project that was known to be essentially impossible for a hundred years is being used as a way to bump the averages here. It is not possible to effectively or reasonably generalize based on the most extreme exception available.